Mercurial > repos > ebi-gxa > scanpy_filter_cells
diff scanpy-filter-cells.xml @ 2:c23d0ff783d4 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d
author | ebi-gxa |
---|---|
date | Fri, 25 Oct 2019 08:25:27 -0400 |
parents | dcfb23758646 |
children | 8e48fa9618c1 |
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--- a/scanpy-filter-cells.xml Mon Sep 16 08:19:52 2019 -0400 +++ b/scanpy-filter-cells.xml Fri Oct 25 08:25:27 2019 -0400 @@ -12,15 +12,15 @@ --gene-name '${gene_name}' #end if #if $parameters - #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters]) + #set pars = ' '.join(['--param c:{name} {min} {max}'.format(**$p) for $p in $parameters]) ${pars} #end if #if $categories - #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories]) + #set cats = ' '.join(['--category c:{name} {values}'.format(**$c) for $c in $categories]) ${cats} #end if #if $subsets - #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $c in $subsets]) + #set subs = ' '.join(['--subset c:{name} {subset}'.format(**$s) for $s in $subsets]) ${subs} #end if @INPUT_OPTS@ @@ -31,14 +31,14 @@ <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="gene_name" type="text" value="index" label="Name of the column in `anndata.var` that contains gene name" - help="This is used for flagging mitochondria genes (starting with 'MT-')"/> + <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name" + help="Used for flagging mitochondria genes (starting with 'MT-'). Leave empty if gene table already has a boolean column called 'mito' that flags MT genes"/> <repeat name="parameters" title="Parameters used to filter cells" min="1"> <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts"> <option value="n_genes">n_genes</option> - <option value="cell:n_counts">n_counts</option> - <option value="pct_counts_mito">pct_counts_mito</option> + <option value="n_counts">n_counts</option> + <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged)</option> </param> <param name="min" type="float" value="0" min="0" label="Min value"/> <param name="max" type="float" value="1e9" label="Max value"/> @@ -46,12 +46,12 @@ <repeat name="categories" title="Categories used to filter cells" min="0"> <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> - <param name="values" type="text" value="" label="Comma-separated values"/> + <param name="values" type="text" value="" label="Comma-separated values to keep"/> </repeat> <repeat name="subsets" title="Subsets used to filter cells" min="0"> <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> - <param name="subset" type="data" format="tabular" label="List of values"/> + <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> </repeat> <expand macro="export_mtx_params"/> </inputs> @@ -72,7 +72,7 @@ <param name="max" value="2500"/> </repeat> <repeat name="parameters"> - <param name="name" value="cell:n_counts"/> + <param name="name" value="n_counts"/> <param name="min" value="0"/> <param name="max" value="1e9"/> </repeat>